|
| Status |
Public on Nov 26, 2014 |
| Title |
PD88.2 |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 human fiboblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: IMR90
cell type: senescent
|
| Treatment protocol |
No treatment.
|
| Growth protocol |
Cells were grown using standard conditions and RNA harvested when plates were 80% confluent
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using RNA easy mini kit. Epicentre Ribodepletion kit was used to deplete ribosomal RNA. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 10 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
ribodepleted RNA
RNA-Seq of PD88 senescent IMR90 cells
Ribodepletion was performed using illumina epicentre Kit and libraires were prepared according to illumina protocol
|
| Data processing |
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 whole genome using tophat 1.4.1 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments), PCR duplicates were removed and subsequent reads piledup and converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base. bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig. bigWig files have PCR duplicates removed.
|
| |
|
| Submission date |
Dec 16, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter D. Adams |
| Organization name |
University of Glasgow, Beatson Institute for Cancer Research
|
| Street address |
Switchback Rd, Bearsden
|
| City |
Glasgow |
| ZIP/Postal code |
G61 1BD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE53356 |
Expression data from PD32 and PD88 IMR90 |
|
| Relations |
| BioSample |
SAMN02444800 |
| SRA |
SRX393064 |
